Annonces

Postdoc offer: Characterization of the Mimiviridae genome organization

 

The employer

Code unité : UMR 7256

Laboratory: Information Génomique et Structurale

Laboratory Head: Chantal ABERGEL

Address: Information Génomique & Structurale - IGS - UMR 7256 CNRS, Aix-Marseille Université

Institut de Microbiologie de la Méditerranée - IMM - FR 3479

163 Avenue de Luminy - case 934

13288 Marseille cedex 09 (France)

Phone: 0491825422

Email: chantal.abergel@univ-amu.fr

Website: http://www.igs.cnrs-mrs.fr/

 

POSITION DESCRIPTION

 

Missions: Characterization of the Mimiviridae genome organization

The IGS laboratory is offering a Post-doctoral position to study the genome organisation of the Mimiviridae inside the icosahedral capsids. The genome is surrounded by proteins allowing the 400 µm long dsDNA to fold as a helicoidal assembly reminiscent of filamentous phages but with a larger section (30nm).This study could reveal possible evolutionary links with other known helicoidal genome structures such as the ones used by phages or archaeal viruses or even with the nuclear chromatin.

 

Activity:

One first aim will be to purify efficiently the rod-shaped structure corresponding to the genomic fiber in order to identify the proteins which are involved in its organization using Mass spectrometry proteomics.

A protocol for releasing it efficiently from the capsids is already available but needs to be optimized. Together with a PhD student, the candidate will then express the individual proteins and determine their 3D-structures by X-ray crystallography or/and Cryo-EM. Co-expression and in vitro reconstitution experiments will also be attempted depending on the genomic fiber protein complexity as revealed by the proteomic analyses. Finally, Cryo-EM structure determination will be conducted on the native genomic fiber and on the in vitro reconstituted genome free structure. The Cryo-EM data acquisition will be performed in collaboration with the Kay Grünewald laboratory, CSSB, Hamburg, Germany). The IGS laboratory possesses all necessary computing power and has access to two imagery platforms in Marseille.

 

Eligibility

 

Constrains: Data acquisition at synchrotron are made in the context of a shared Bag which means that the applicant will have to spend time on the beamlines collecting data for the IGS but also for other members of the BAG. Missions are not frequent but can take place during nights and week-end.

 

 

The employer – The Laboratory Information Génomique et Structurale (IGS)

 

 

 

The IGS laboratory is a pioneer and a world leader in the study of giant viruses for which we discovered the four known families. A unique strength of the IGS laboratory is the coexistence of a computational biology team and an experimental biology team, allowing efficient and seamless continuity from isolation of new microorganisms to their comprehensive characterization using genomics, transcriptomics and proteomics. The laboratory also has the capacity to determine the 3D-structure of viral proteins of specific interest using X-ray crystallography alone or in combination with Electron Microscopy. An ERC advanced grant starting in October 2019 provides two post-doctoral positions and two PhD grants to study the structural organization of the genomes of the Mimiviridae and identify the machinery responsible for their packaging into rod shaped structures filling the 450nm icosahedral virions.

 

 

IGS Resources

 

The IGS laboratory is already well equipped for cellular biology (2 L2 rooms, 6 PSM, 3 fluorescence microscopes (including 1 Zeiss Axio), 4 incubators), biochemistry (PCR, 1 Microbiology PSM, 3 incubators, 2 Aktä explorer 10S, 1 Aktä 3D, 1 Aktä Prime, Nanodrop, Qubit, 96-well and 1mL spectrophotometers), and structural biology (Mosquito crystallization robot, in-house diffractometer (Oxford diffraction Xcalibur PXUltra, a speedvac SPD131 ThermoFischer). The IGS has direct access to the 12 technical platforms at the Mediterranean Institute of Microbiology (IMM, AMU-CNRS FR3479, Staff: 300). The platforms of interest for the project are fluorescence/TEM imaging (TEM, Cryo-TEM), NMR (600 MHz, cryoprobe), Proteomics, protein expression and protein interaction facility (1 Aktä prime, 1 Aktä Pure). The protein production platform runs a Blitz system used to rapidly screen and characterize macromolecular interactions. The IGS also has permanent access to the Luminy campus imagery platforms including electron microscopy (TEM and STEM) at the IBDM (Institut de Biologie du Développement de Marseille). The IGS masters all the required skills in cellular biology (light, fluorescence and electron microscopy, virus purification, synchronized infections, extraction, and molecular studies), structural biology, biochemistry and virology methods. The laboratory is also part of the Marseille synchrotron BAG and has access to European synchrotron radiation facilities and Soleil for crystallography. The Bag also provides free of charge access to the EM platforms at ESRF equipped with Titan Krios cryo-electron microscope with K2 Summit direct electron detector, a Quantum LS imaging filter and a Volta phase plate (VPP). This microscope will be run as a beamline (CM01) within the Partnership for Structural Biology (PSB) together with the microscopes located at IBS and EMBL. The Cryo-EM data acquisition will be performed in collaboration with the Kay Grünewald laboratory, CSSB, Hamburg, Germany equipped with five electron cryo-microscopes, including 2 Titan-Krios (300 keV top end, autoloader, DED, energy filter, VPP). The IGS laboratory possesses all necessary computing power (cluster with 71Nodes, 156 CPU, 828 Cores, 4700 Go, 150 To).

 

 

Application process:

To apply for the Position at IGS, the candidate must give his/her CV with a complete list of publications, a motivation letter and at least one reference letter at http://bit.ly/2RQ1rlk.

 

 

The selected candidate can start between the end of October 2019 and January 2020, depending on his/her availability. The position is for 1 year and can be renewed for 3 years.

 

 

Monthly Salary between 2750 and 3840 € depending on experience

 


Postdoc offer: Structural and functional characterization of the machinery used by the Mimiviridae to compact their genomes

The employer

Code unité : UMR 7256

Laboratory: Information Génomique et Structurale

Laboratory Head: Chantal ABERGEL

Address: Information Génomique & Structurale - IGS - UMR 7256 CNRS, Aix-Marseille Université

Institut de Microbiologie de la Méditerranée - IMM - FR 3479

163 Avenue de Luminy - case 934

13288 Marseille cedex 09 (France)

Phone: 0491825422

Email: chantal.abergel@univ-amu.fr

Website: http://www.igs.cnrs-mrs.fr/

POSITION DESCRIPTION

 

 

Mission: Structural and functional characterization of the machinery used by the Mimiviridae to compact their genomes

 

The IGS laboratory is offering two Post-doctoral positions and to PhD thesis grants in the context of and ERC grant. The present position will aim to elucidate how the Mimiviridae genome is packaged inside the icosahedral capsids. As the disorganized DNA is packaged through at least one lipidic membrane into a rod-shaped helicoidal structure with a 30nm section, a specific assembly machinery must be devoted to the genome packaging. The ultimate goal of the project will be to compare this machinery with the DNA translocation machineries used in the cellular and the viral world.

 

Activité

The first aim of the project will be to extract the membrane from the capsids to identify the membrane anchored proteins (viral and cellular). Mimivirus genome encodes a DNA packaging ATPase that was proposed to be involved in genome packaging. It is one of the few core genes conserved in all Nucleocytoplasmic large DNA viruses. Moreover, this ATPase is a closer homolog to prokaryotic chromosome segregation motors than to other viral packaging motors, such as large terminase. The Packaging ATPase will thus be studied alone and will be used as a bait to identify its possible partners, in vitro and in infected cells. Together with a PhD student, the candidate will then express the individual proteins and will use standard methodologies including the use of nanodiscs, crystallization and single particle Cryo-EM to retrieve structural information of individual proteins and complexes. In vitro reconstitutions of complexes will also be performed.

 

Compétences

 

 

The employer – The Laboratory Information Génomique et Structurale (IGS)

 

The IGS laboratory is a pioneer and a world leader in the study of giant viruses for which we discovered the four known families. A unique strength of the IGS laboratory is the coexistence of a computational biology team and an experimental biology team, allowing efficient and seamless continuity from isolation of new microorganisms to their comprehensive characterization using genomics, transcriptomics and proteomics. The laboratory also has the capacity to determine the 3D-structure of viral proteins of specific interest using X-ray crystallography alone or in combination with Electron Microscopy. An ERC advanced grant starting in October 2019 provides two post-doctoral positions and two PhD grants to study the structural organization of the genomes of the Mimiviridae and identify the machinery responsible for their packaging into rod shaped structures filling the 450nm icosahedral virions.

 

IGS Resources

The IGS laboratory is already well equipped for cellular biology (2 L2 rooms, 6 PSM, 3 fluorescence microscopes (including 1 Zeiss Axio), 4 incubators), biochemistry (PCR, 1 Microbiology PSM, 3 incubators, 2 Aktä explorer 10S, 1 Aktä 3D, 1 Aktä Prime, Nanodrop, Qubit, 96-well and 1mL spectrophotometers), and structural biology (Mosquito crystallization robot, in-house diffractometer (Oxford diffraction Xcalibur PXUltra, a speedvac SPD131 ThermoFischer). The IGS has direct access to the 12 technical platforms at the Mediterranean Institute of Microbiology (IMM, AMU-CNRS FR3479, Staff: 300). The platforms of interest for the project are fluorescence/TEM imaging (TEM, Cryo-TEM), NMR (600 MHz, cryoprobe), Proteomics, protein expression and protein interaction facility (1 Aktä prime, 1 Aktä Pure). The protein production platform runs a Blitz system used to rapidly screen and characterize macromolecular interactions. The IGS also has permanent access to the Luminy campus imagery platforms including electron microscopy (TEM and STEM) at the IBDM (Institut de Biologie du Développement de Marseille). The IGS masters all the required skills in cellular biology (light, fluorescence and electron microscopy, virus purification, synchronized infections, extraction, and molecular studies), structural biology, biochemistry and virology methods. The laboratory is also part of the Marseille synchrotron BAG and has access to European synchrotron radiation facilities and Soleil for crystallography. The Bag also provides free of charge access to the EM platforms at ESRF equipped with Titan Krios cryo-electron microscope with K2 Summit direct electron detector, a Quantum LS imaging filter and a Volta phase plate (VPP). This microscope will be run as a beamline (CM01) within the Partnership for Structural Biology (PSB) together with the microscopes located at IBS and EMBL. The Cryo-EM data acquisition will be performed in collaboration with the Kay Grünewald laboratory, CSSB, Hamburg, Germany equipped with five electron cryo-microscopes, including 2 Titan-Krios (300 keV top end, autoloader, DED, energy filter, VPP). The IGS laboratory possesses all necessary computing power (cluster with 71Nodes, 156 CPU, 828 Cores, 4700 Go, 150 To)..

 

 

 

Application and selection process :

 

To apply for the Position at IGS, the candidate must deposit his/her CV with a complete list of publications, a motivation letter and at least one reference letter at http://bit.ly/2RKaWm1.

 

The selected candidate can start between the end of October 2019 and January 2020, depending on his/her availability. The position is for 1 year and can be renewed for 3 years.

 

Monthly Salary between 2750 and 3840 € depending on experience

 

Open job position in molecular pharmacology Expert on ion channels

 

DOMAIN THERAPEUTICS, based in Strasbourg and Montreal, is a biopharmaceutical company researching and developing new drugs acting on transmembrane proteins. Initially focused on G protein-coupled receptors, the company is now extending its scope to other transmembrane proteins.

 

At the heart of the Innovation Park from Strasbourg, DOMAIN THERAPEUTICS offers opportunities to develop your skills, to collaborate on drug discoveryprojects and to contribute to therapeutic innovations.

 

In this context, DOMAIN THERAPEUTICS is seeking a highly motivated:

 

Researcher in molecular pharmacology, with a strong expertise on ion channels

 

As part of the R&Dof DOMAIN THERAPEUTICS, the researcher will have for main missions to:

-Develop and apply new concepts on ion channels-Lead new projects and guide strategic choices-Collaborate with otherscientists within Domain and with French or international academic labs

-Ensure the implementation of SOP and flow sheets-Supervise technicians and / or engineers to enable the realization of biological experiments in a reliable, reproducible and timely manner

-Participate actively in group meetings

-Promote the image of the company by presenting results at international conferences or by writing scientific articles

 

More precisely, the candidate must have:

-A solid background on ion channels, validated by a PhD and a post-doc position

-Good knowledges in electrophysiology, in cellularand molecular biology(sub cloning, PCR...), cell culture (cell line maintenance, transfection....), cellular assays, biochemistry (ELISA, WB,...)

-Ability and willingness to perform the assays (functional, binding assays; FRET and BRET technologies), to analyze the experiments, understand the results and act accordingly-Proven organizationalskills and ability to plan ahead, set priorities and workto deadlines

-A very good team spirit and integration capacity with the ability to be proactive in solving problems

 

You have a PhD in biology, with 1 to 2 years of experience, ideally with an international experience, you know how to adapt to challenges and highlight rigor, method, dynamismand creativity, you have an appetite for taking responsibility, you want to evolve in a growing structure, within a young and dynamic team, where your creativity will be valued, then join us! The position (permanent position) is to be filled as soon as possible.

 

Contact :

 


Please send CV and motivation letter by email

Address: Domain Therapeutics -BioParc –850 Bld Sébastien Brandt -67400 Illkirch

Email: contact@domaintherapeutics.com

Website: http://www.domaintherapeutics.com


 

Thesis: Identification of structural patterns for antimicrobial peptides recognition at the bacterial cell-­‐wall level

Astrid Walrant (astrid.walrant@sorbonne-­‐universite.fr), Emmanuelle Sachon (emmanuelle.sachon@sorbonne-­‐universite.fr) UMR 7203, Laboratoire des BiomoléculesPôleAnalyse interactions moléculaires et cellulairesSorbonne Université, Paris. ED 406, Chimie moléculaire de Paris Centre (http://www.ed406.upmc.fr/fr/contrats-­doctoraux.html)

 

Membrane-­‐active peptides are a broad class of small peptides with unique membrane interaction properties. Amongst them, cell-­‐penetrating peptides (CPPs) and antimicrobial peptides (AMPs) are of particular interest.

 

Although most AMPs are usually indifferently active on Gram-­‐positive and Gram-­‐negative bacteria, some are more specifically targeted. We recently showed that the AMP DMS-­‐DA6, isolated from a Mexican frog, kills Gram-­‐positive bacteria very specifically (Cardon et al. 2018).

 

The selectivity of AMPs towards bacterial membranes cannot be only the consequence of simple electrostatic interactions between cationic residues on the peptide and anionic lipids. Indeed, both types of bacteria have a negatively charged membrane. Nevertheless, their cell walls differ greatly in terms of surface glycoconjugates. In the case of Gram-­‐positive bacteria, a very thick layer of peptidoglycan (PGN) is found in the most outer part of the bacteria.

 

We recently showed that DMS-­‐DA6 could interact with PGN and that this interaction could potentiate the effect of DMS-­‐DA6 on a lipid bilayer (Cardon et al. 2018). However, so far, we only have indirect evidence for this interaction. Our first objective would thus be to obtain direct evidence of this interaction in vitro. Building on this, our second aim is to identify the structural patterns involved in peptide/PGN and peptide/PGN/lipids using affinity photocrosslinking on reconstituted models. The next step up would then be to evidence interactions on live bacteria.

 

1) In vitro characterisation of DMS-­‐DA6/PGN interaction

 

We plan to study this interaction using various tools that are all available within the host lab, in particular fluorimetry, co-­‐sedimentation assays and isothermal titration calorimetry (ITC). The host team has excellent expertise in this kind of in vitro approach (Walrant et al. 2017).

 

2) Identification of structural recognition patterns by affinity photocrosslinking coupled to mass spectrometry (MS)

 

Affinity photocrosslinking is a powerful technique to study interaction partners, isolate covalent complexes and identify key recognition motifs. Herein, we will develop two complementary approaches to study the interaction partners of DMS-­‐DA6 in either binary systems (peptide/PGN or peptide/membrane) or ternary systems (peptide/PGN/membrane).

 

In the first approach, we will design a DMS-­‐DA6 sequence that will carry a benzophenone (Bzp) photoprobeand a biotin for complex purification and enrichment. We successfully used this type of approach to study the interaction of cell-­‐penetrating peptides (CPPs)and lipids (Jiao et al. 2017, Bechtella et al. submitted). With this approach, our aim is to identify and characterise specific regions interacting with DMS-­‐DA6 on PGN (or PGN analogues) and/or lipids.

 

In the second approach, we will use bi-­‐functionnal lipids, carrying a photoactivable diazirine and analkyne moiety that can be functionalised by click-­‐chemistry (Haberkant et al. 2013). We have recently implemented this approach in our team and are obtaining very promising results with CPPs. This approach is adaptable to any AMP without sequence modification.

 

3 )Photoaffinity crosslinking on live cells

 

Once we have fully characterised the interactions on reconstituted systems, we will move up to partner identification on live bacteria either with the peptide-­‐Bzp or the bi-­‐functionnal lipid strategy. A live cell environment is necessarily more complex, therefore, partner identification in such a context will be challenging.

 

This project should yield valuable information on AMP/PGN/lipids interactions. It will give insighton the general mechanism of membrane permeation by AMPs. It shouldhelp predict the activity of AMPs on bacterial strainsand enable us to rationalise the design of new AMPs with optimised sequences for better bacteria targeting.

 

This project is at the interface of chemistry, biochemistry and biophysics and will involvea large set of techniques: peptide synthesis, mass spectrometry, cell culture, model membranes, calorimetry etc...all available at the host laboratory (LBM).This PhD project will be supervised by Emmanuelle Sachon (HDR) and Astrid Walrant, whose expertise encompassmass spectrometry, affinity photolabelling, membrane active peptides and characterisation of biomolecular interactions.

 

References

 

Bechtella, L., Kirschbaum, C., Clodic G., Matheron, L., Bolbach, G., Sagan, S., Walrant A., Sachon, E., ‘Benzophenone photoreactivity with lipid membranes: simple system, complex information’,

 

Submitted Cardon, S., Sachon, E., Carlier, L., Drujon, T., Walrant, A., Aleman-­‐Navarro, E., Martinez-­‐Osorio, V., Guianvarc’h, D., Sagan, S., Fleury, Y., Marquant, R.,Piesse, C., Rosenstein, Y., Auvynet, C. and Lacombe, C. (2018) ‘Peptidoglycan potentiates the membrane disrupting effect of the carboxyamidated form of DMS-­‐DA6 , a Gram-­‐positive selective antimicrobial peptide isolated from Pachymedusa dacnicolor skin’, PLoS ONE, 13(10), p. e0205727.

 

Haberkant, P., Raijmakers, R., Wildwater, M., Sachsenheimer, T., Brügger, B., Maeda, K., Houweling, M., Gavin, A., Schultz, C., Meer, G. Van, Heck, A. J. R. and Holthuis, J. C. M. (2013) ‘In Vivo Profiling and Visualization of Cellular Protein –Lipid Interactions Using Bifunctional Fatty Acids’, Angewandte Chemie -­‐International Edition, 52(14), pp. 4033–4038. doi: 10.1002/anie.201210178.

 

Jiao, C. Y., Sachon, E., Alves, I. D., Chassaing, G., Bolbach, G. and Sagan, S. (2017)‘Exploiting Benzophenone Photoreactivity To Probe the Phospholipid Environment and Insertion Depth of the Cell-­‐Penetrating Peptide Penetratin in Model Membranes’, Angewandte Chemie -­‐International Edition, 56(28), pp. 8226–8230. doi: 10.1002/anie.201703465.

 

Walrant, A., Cardon, S., Burlina, F. and Sagan, S. (2017) ‘Membrane Crossing and Membranotropic Activity of Cell-­‐Penetrating Peptides: Dangerous Liaisons?’, Accounts of Chemical Research, 50(12), pp. 2968–2975. doi: 10.1021/acs.accounts.7b00455.

Postdoctoral Scientist – Neurobiology
Salary Range £30,914 – £33,755
MRC Laboratory of Molecular Biology, Cambridge, UK

The MRC Laboratory of Molecular Biology is one of the birthplaces of molecular biology and is an internationally renowned centre for fundamental biomedical research.

 

The LMB has a strong track record in training Postdoctoral Fellows who have gone on to become leading Scientists. We also have an excellent record of innovative basic research leading to applications in medicine. Scientists are drawn to the LMB from all over the world, thus creating a lively and international community for the exchange of ideas and technical innovation. Following our move to a new laboratory in 2013, we are able to provide state-of-the-art facilities in which innovative medical research, translation and collaboration can flourish.

 

Applications are invited for a Postdoctoral Scientist position in the group of Dr Ingo Greger to study synaptic glutamate receptor complexes using cryo-electron microscopy (cryo-EM).

 

This project builds on our recent cryo-EM work on heteromeric AMPA-type glutamate receptors (Herguedas et al., Science 2016; Herguedas et al., Science 2019). Candidates should have a PhD and experience with cryo-EM; expertise in membrane protein biochemistry would be greatly advantageous.

 

Successful applicants will be awarded a 3-year Career Development Fellowship/MRC Postdoctoral Training Scheme. The fellowship is a training and development position for a post-doctoral scientist who has recently completed their doctoral studies, or is moving into a new research discipline.

 

Working for UKRI MRC provides a whole host of benefits including a defined benefit pension scheme, excellent holiday entitlement (40 ½ days including bank holidays and privilege days) and Benenden Healthcare membership. You will also have access to employee shopping/travel discounts, on site sport and social facilities, as well as salary sacrifice cycle to work schemes and childcare vouchers.

 

For further information of the research undertaken at the LMB, please visit:
http://www2.mrc-lmb.cam.ac.uk

 

Informal enquires may be made to Dr I. Greger (ig@mrc-lmb.cam.ac.uk).

 

To apply and access full details of the vacancy please visit our job board at https://mrc.tal.net/vx/lang-en-GB/appcentre-1/candidate/postings/1184 . If you are unable to apply online please contact us at recruit@mrc-lmb.cam.ac.uk.

 

Closing date: 29 April 2019
Final appointments will be subject to a pre-employment screening.
The Medical Research Council is an Equal Opportunities Employer who participates in the Disability Confident scheme.

 

Postdoctoral Position: Biomolecular Solid-state NMR

 

The laboratory Membrane Biophysics and NMR at the University of Strasbourg has an opening for a postdoctoral position with experience in using solid-state NMR for the analysis of peptides and proteins. The aim of the project is to reveal the structural determinants that define the highly specific lipid recognition motif of a transmembrane protein and to characterize changes in structure, dynamics, oligomerization and topology of the protein as well as the lipids during recognition. Another ongoing project is the structural investigation of peptide fibers with strong nucleic acid and lentiviral transfection potential.

 

Candidates should have good experience in biomolecular solid-state NMR. Other techniques of the laboratory are solution NMR approaches, various types of biophysical methods, peptide synthesis and/or the biochemical production of proteins. Knowledge in some of these latter techniques are of advantage. S/he should have an interest in working in a highly interdisciplinary, international and collaborative environment. The project and position are funded by a three-year grant from the French National Agency for Research (ANR). The University of Strasbourg chemistry, life sciences and structural biology departments have excellent scientific records, with a multitude of collaborations world-wide.

 

Strasbourg is a very nice city on the French side of the Rhine river, at the border to Germany, with easy access to nearby mountains (Vosges, Black Forrest, Alps). Being in the heart of Europe it takes only short train rides to multiple destinations of scientific and/or touristic interest.

 

Candidates should send their CV, publication list and contact info for three references to:

 

Prof. Burkhard Bechinger,

bechinger@unistra.fr

Web Sites: www-chimie.u-strasbg.fr/~rmnmc

www.icfrc.fr/en/

 

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